X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterfragmentscommand.h;h=ee25fb30da91c4ab338b0b173bcf05a6f1689c81;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=9bdbc4479f19bd7e1aa8297ed4e1f278e0de912f;hpb=61798fe609675abfedf511e542cc48c56a531199;p=mothur.git

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index 9bdbc44..ee25fb3 100644
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "sequence.hpp"
+#include "counttable.h"
 
 /************************************************************/
 struct seqRNode {
@@ -31,21 +32,36 @@ class ClusterFragmentsCommand : public Command {
 	
 public:
 	ClusterFragmentsCommand(string);
-	~ClusterFragmentsCommand();
-	int execute();	
-	void help();
+	ClusterFragmentsCommand();
+	~ClusterFragmentsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "cluster.fragments";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
+	string getDescription()		{ return "creates a namesfile with sequences that are a fragment of a larger sequence"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
+    CountTable ct;
 	bool abort;
-	string fastafile, namefile, outputDir;
+	string fastafile, namefile, countfile, outputDir;
+	int diffs, percent;
 	vector<seqRNode> alignSeqs; 
 	map<string, string> names; //represents the names file first column maps to second column
 	map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
 	map<string, int>::iterator itSize; 
+	vector<string> outputNames;
 	
 	int readFASTA();
 	void readNameFile();
 	void printData(string, string); //fasta filename, names file name
+	bool isFragment(string, string);
 	
 };